SVS Bone Lipid LCM processing

Processing

• run.m – project name, call batch files
• lcm_batch.m - retrieve all studies, dates, and subjects
  • svs_press_lipid_lcm.m per sequence - run LCM

Basis file for LCModel included at LCM_basis/gamma_press_te30_123mhz_106.basis

LCModel

see https://github.com/LabNeuroCogDevel/MRSIcoord.py/blob/master/Makefile#L23 for building LCModel from source.

output like

Raw DICOM

For example, see data/FAZ-BMAT/A01_2022.10.12-10.24.51/.

Sequences are (sequence number and names are fixed)

svs_se_30_Femur_Epiphysis_0x0.8     # SVS DICOM
svs_se_30_Femur_Epiphysis_ref_0x0.7 # ROI three orthogonal slices

svs_se_30_Femur_Metaphysis_0x0.10
svs_se_30_Femur_Metaphysis_ref_0x0.9
svs_se_30_Femur_midDiaphysis_0x0.18
svs_se_30_Femur_midDiaphysis_ref_0x0.17
svs_se_30_L4_0x0.27
svs_se_30_L4_ref_0x0.26
svs_se_30_Liver_0x0.35
svs_se_30_Liver_ref_0x0.34

On Gyrus /disk/mace2 files are found like

scan_data/$Propject/$StudyDate/$Subject/svs_*/
scan_data/FAZ-BMAT/2024.08.16-10.15.00/C06/svs_*/